There is a stall switch on the shift linkage on the motor. This may be causing the problem if not properly adjusted. The stall switch is designed to stall the engine for a brief second while the outdrive is going in or out of gear. This is special to the Alpha 1 drives.
Also, it could be the lower shift cable. The cable will wear over time, then it drags and doesn't move where its supposed to, that's why it stalls out the motor. It could be your shift cable might be a bit sticky or in need of adjustment. Though I have heard, depending on the age of the cable, it should not be adjusted - it needs replaced... This was the case on Jasons boat and is why his cable was replaced.